


When The Doctor Loves The Government

by Mycrofts_Favorite, TheDoctorsDetective



Category: Doctor Who, Sherlock (TV)
Genre: Abandonment, Fluff and Angst, M/M, Relationship Problems, companion - Freeform
Language: English
Status: In-Progress
Published: 2014-08-16
Updated: 2014-09-01
Packaged: 2018-02-13 11:27:56
Rating: Not Rated
Warnings: No Archive Warnings Apply
Chapters: 3
Words: 4,082
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2149041
Author URL: https://archiveofourown.org/users/Mycrofts_Favorite/pseuds/Mycrofts_Favorite, https://archiveofourown.org/users/TheDoctorsDetective/pseuds/TheDoctorsDetective
Summary: <blockquote class="userstuff">
              <p>Twenty years ago, after their parents left, Mycroft Holmes was raising his 13-year-old brother Sherlock and his 3-year-old sister Alissa. After just five months of being a single "parent," going to law school, and working the late shift at his job, Mycroft is completely burned out. At least until the Doctor shows up and invites the small family of three to travel in his TARDIS. Mycroft and the Doctor fall in love with eachother, the both of them now raising the two children, and promise that nothing will ever separate this makeshift family. One day, during a terribly dangerous encounter with Daleks, the Doctor orders the Holmes's into the TARDIS and sends them back to the manor for safety. They exit the TARDIS back home, expecting the Doctor to come back for them soon. The TARDIS disappears and Mycroft never sees it again, leaving him in a puddle of sadness. Now, in the present, Mycroft runs into the Doctor on his way back to his office after a meeting, and the following story ensues.</p>
            </blockquote>





	1. The Reuniting

The two men accidentally ran into each other outside of a large Government building. "Sorry," said one. "I'm John Smith." He held out his hand for the other man to shake.

"Mycroft Holmes, pleasure," the slightly taller man said, shaking John's hand.

"Mycroft?" Said John, stunned.

"Yes, that is my name. Do we know each other? I must apologize, I meet many people each day and it is hard for me to keep everyone straight," Mycroft said.

"I haven't seen you in ages! How have you been? Is Sherlock still into pirates? Come get into the TARDIS, there is a weeping angel infestation in Surry and I need your help," the first man rambled.

"I know, I have eyes everywhere, wait, how do you know about Sherlock and weeping angels? And how the hell do you have a TARDIS?" Mycroft demanded. John looked at Mycroft as if to remind him of something. "Wait, Doctor? Where the hell have you been! I've been waiting twenty years! Twenty years, my eyes all over the country, keeping out for your TARDIS," he said, bordering on angry.

"I, I'm sorry Mycroft," The Doctor said shyly.

"You didn't even write," Mycroft said. This time, he sounded hurt.

"Well," the Doctor gave a nervous sort of laugh, "through time, that's sort of hard."

"I met this nice chap, name's Jack Harkness, says he traveled with you a while back. Were you trying to replace me or something?" Mycroft was once again raging and demanding. The pair had made their way up to Mycroft's office where they could talk in privacy.

"You, um, you met Jack?" The Doctor asked nervously.

"Of course I met Jack."

"Oh no, did he tell you about, ummm, did he tell you about that?" he asked once again.

"About what, Rose? Because yes." Mycroft stated.

"No, about Torchwo-" the Doctor cut his sentence short.

"Yes, I know about Torchwood, eyes and ears all over the country, remember?" Mycroft replied  
"But Torchwood is WAY beyond the government, you weren't supposed to know about that."

"Yes, but I have my ways." The Doctor was obviously getting nervous now, realizing he was falling short in this argument.

"Yeah, well don't think I don't know about Greg," The doctor changed the subject.

Mycroft looked utterly confused. "Who the hell is Greg?" He demanded.

"Oh, like you don't know." He retorted. Mycroft flashed him one of the classic Holmes looks that seemed to say 'no, I honestly don't' "Wait, oh, sorry, that's in the future." He grinned embarrassedly.

"Damn you, Doctor." Mycroft said with an exasperated tone. "Twenty years, Doctor. I've met all of them. The Williams' and I go for brunch every other month. And this Martha girl is quite clever, works almost directly for me now."

"Martha?!" The Doctor demanded. "So that's why she left me, you, Mycroft. You!"

"What the hell, you know I don't 'swing that way,' to put it in the words of Captain Jack." Mycroft said, very annoyed.

"Captain who? He's not a captain, he's a fraud." The Doctor said.

"You know what I mean," Mycroft said. "I don't go out with women."

"Ah, I had an android once," The Doctor said in attempt to change the subject. "Man, are they clingy."

"Tis a shame though, poor donna. I've kept a special eye on her." Mycroft said, obviously not wanting to change the subject.

"What do you mean, what have you done to her?" The Doctor's eyes flashed with rage and fear.

"You hung the poor girl out to dry! I've been protecting her, making sure nothing happens to her!" Mycroft yelled. His voice softened, "I could never hurt you."

"Hurt me?" The Doctor was confused. "How would that work?"

"You get attached," Mycroft began to explain. "If something were to happen to any of these girls, it would kill you. Don't think I didn't hear about what happened with Rose."

"Rose," the Doctor sighed. "She's gone, Mycroft. I couldn't help her."

"I know, and that's how I know if anything were to happen to any of your, oh what were we called, 'companions,' you'd be crushed."

"We?" The Doctor asked.

"Your companions, Doctor!" Mycroft shouted. "Have you not been listening? I know about everyone. Everyone before me, everyone after me."

"Not everyone," the Doctor said, giving him a sly grin.

"What the hell do you mean by that?" Mycroft demanded, only to be answered with an increased slyness of the Doctor's grin. "There are more? People you've forgotten about? Promised to come back to, but never did?" This wiped the grin off of the Doctor's face, and replaced it with shame. "Talk to me, Doctor. You're obviously hiding something, and I want to know."

Silence.

"Tell me Doctor, now." Mycroft was demanding. 

The Doctor gave him a serious stare. "No," he stated simply.

"Doctor, if you don't tell me, I swear…" Mycroft demanded again. "Twenty years, I have waited twenty years." He turned and looked out the window.

"Don't talk about twenty years ago," the Doctor said.

"If you owe me nothing more, you owe me at least this!" Mycroft said loudly, voice filled with sadness. A deep, sad silence filled the room. "Please, Doctor." Mycroft's voice broke the thick quiet. He was almost in tears.

"Mycroft, I-" The TARDIS materialized into the room.

"Doctor, is there someone else in that TARDIS right now?" Mycroft was crying tears of rage.

"Mycroft…" the Doctor exhaled and looked defeatedly at the ceiling, as if praying for help.

"What is it, who's in there?" Mycroft asked, still crying.

"No one," the Doctor said, fake honesty written all over his face.

"I don't believe it." Mycroft pulled a chain out from his shirt, the same one still holding his key to the TARDIS from all those years ago. Telltale guilt was spreading out over the face of the Doctor. "Doctor, you don't- I thought you'd come back for me! I thought, that after twenty long years, you'd finally come back for me. Who are they, I want to know." Mycroft looked more hurt that the Doctor had lied to him, than forgotten him.

"I can't…" the Doctor tried to say. Mycroft walked over to the TARDIS and opened the door, only to have the Doctor step out in front of him. "Mycroft!" the Doctor exclaimed, somehow surprised that Mycroft would just go and look.

Mycroft shoved the Doctor out of his way and walked, steps heavy with anger, into the TARDIS. The Doctor followed briskly. "Who are they, who's life are you ruining now?" A completely enraged Mycroft demanded.

"No!" the Doctor shouted.

"Doctor!" Mycroft hollered back.

"Mycroft, stop," the Doctor said, walking in front of Mycroft and looking at him seriously. "I couldn't-"

"You couldn't what," Mycroft demanded once again. "What couldn't you do?"

"I- Mycroft." The Doctor said. Mycroft was becoming fed up with this lack of answers.

"Tell me now!" Mycroft almost screamed.

"I can't!" The Doctor replied, also raising his voice.

"Why not," Mycroft yelled. "Because you don't want to hurt me? It's a little goddamned late for that!" He looked at the Doctor and could tell he was digging throughout his mind for excuses. "Excuses aren't going to work, sweetie." The Doctor looked confused at his choice of words. "Oh, you thought I didn't know about River Song, didn't you."

"She's not here, I- I lost her." The Doctor said sadly.

"You married her!" Mycroft shouted.

"And I lost her!" The Doctor shouted back.

"You said you were going to marry me!" Mycroft yelled. "I'd damn well rather be lost than forgotten! Because you don't choose to lose someone. Forgetting someone though," he was hurt and furious.

"Mycroft," the Doctor said solemnly. "I couldn't come back for you, I'm sorry. Timey wimey stuff, can we forget about that now? Please?"

Mycroft shook his head, "I want an explanation, please, Doctor. Just a tiny one?" Just then, Mycroft noticed a lock of long, curly, sepia brown hair drift around the corner and pointed. "Doctor, who's that?" The Doctor panicked as he turned around to look. You know what, don't even bother." The Doctor looked into Mycroft's eyes as innocently as possible. "Goodbye, Doctor. Don't hurt her like you did me." He turned around to leave, but was stopped when his ex placed a gentle, but firm hand on his arm.

"Mycroft, she's your sister."


	2. Love, Pain, Sacrifice

“Lissy?” Mycroft said surprised and a little bit hurt.  
“I’m sorry Mycroft, I really am.” Mycroft was coming back to his senses now.   
“You left me. For my sister?”   
“Mycroft-” The Doctor tried to explain. Mycroft starts moving in toward the Doctor.   
“You. You’re pathetic, ya know that?”   
The girl came out from behind a T.A.R.D.I.S support structure, “Don’t I get a say in this?” She cut in.  
“Get a say in what? My best friend leaves me for my 23 three year old sister. My pretty sister.” Mycroft says with a hint of disappointment.   
“But Mycroft. It isn’t like that.” Mycroft laughs sarcastically. “You aren’t listening Mycroft. And you Doctor? You aren’t telling.” The Doctor slowly spins around, stressing in the background. Alissa points to her brother and the Doctor, “You two, sort it out.” She takes a step back, feeling proud of herself, but is cut short when Mycroft takes charge. “No, Alissa Mae Holmes, you walk out those doors right now. You go straight to the address 221b Baker Street, and you wait for my call.”  
“But Mycroft!” He gives her a stare saying there is no winning this one. Alissa fights back though, “Mycroft, I am pretty sure you’re not my mother.” He just replies calmly, “This is for your own good.”  
“How? Tell me. How?”  
“Trust me. You don't want to be in the same position as me.” Mycroft looks into Alissa’s hazel eyes, “It hurts.”  
“Mycroft, it isn’t your decision to make.”  
“Alissa, please. I'm trying to protect you. That's what the Doctor want's isn't it? For his companions to be safe?” Alissa nods, accepting defeat. The Doctor starts pointing and gesturing to a corner, “I’ll just-I’ll be-uh-over...There.” Mycroft turns to the Doctor and point’s to a spot next to himself on the floor, “No, you. Come stand here. This will be momentary.” The Doctor obeys. Mycroft turns back to his sister. “ I raised both you and Sherlock. I still have two rooms in the Manor filled with pirates and princesses. You haven't listened to me once, but if ever there is a time to obey me, it's now.” Mycroft is serious and Alissa realizes this, she heads to the doors. She turns back to look at Mycroft. He catches her, “We'll talk later. I promise. But for now, please just go.” Mycroft watches to make sure she leaves, then texts one of his people to ensure she gets to the flat of his brother and brother-in-law safely and efficiently. He looks to the Doctor, “I’m ready to listen, now.”   
The Doctor nervously smiles, “Heh...”   
“I promise to let you talk and I will not input until you say you are done speaking.” The Doctor nods in response.   
“Well, for starters,” He says regaining some of his lost dignity. “We aren’t going to be standing here the whole time.” And gestures over to the bench. Mycroft follows and sits next to his ex. “So, twenty years then, huh?” Mycroft nodded. “I am sorry though, I really am. You see, the Orbit Nebulizer, it’s what coordinates the T.A.R.D.I.S. from one place and time to another. It broke. We can still get this old police box places, but they won’t always be correct until I fix the Orbit Nebulizer.” Mycroft looks confused. “I found your sister…” The Doctor’s face now filled with sorrow. “Did you notice anything different about her? Something that wasn’t there the last time?”  
“Doctor, I haven’t seen her for five years. Alissa left when she was 18.”   
“But you must at least remember her?” The Doctor sighed. “She’s dying.”  
“She was, wait- What?” He heard him though. It was a rhetorical question.  
“She doesn’t remember everything. Most of her memory was rescued, but to her, she hasn’t been gone five years.” Mycroft is very concerned now, just wishing that the Doctor was lying.  
“Doctor. What has happened to my baby sister?”   
“She’s fine, I made sure of that. Every once in a while though, on occasion, She will just stare into nothingness. And whatever it is she is looking at, it frightens her. Mycroft.” He was calm. Mycroft didn’t understand how he could be at a time like this.   
“Doctor?”  
“Yes?”  
“What test’s have you run?”  
“All of them. Nothing shows up.”   
“If you can recall, the same would occasionally happen to Sherlock while he was battling his addiction. Staring into space in fear, the mere minutes of memory retention. But he wasn’t dying.” He looked down to his hands sitting in his lap.   
“Mycroft. The thing is...Alissa, she shouldn’t even be alive.” Mycroft quickly looked up at the Doctor. The Doctor continued, “I-” He paused thoughtfully. “I gave her one of my regenerations.   
“What does that mean?!” The Doctor could see that Mycroft was getting anxious. “Could it have copied some of your memories, about the war and things?”  
“No. She has none of my memories, but she has some of the vortex energy burning inside her....What she sees, is real to her. She can't retain it because she isn't meant too.”   
“This is, it's the same ordeal that happened with Donna, isn't it?”  
“No.With Donna. She became part of me. She was.Half Time lord. I had to erase her memories or she would have burned. There was nothing else I could do.”  
“Yes, but the regenerations are part of you, aren’t they part Time lord as well?”  
“Maybe,” The Doctor thought it over. “But not in that way. I mean, a regeneration, remakes every cell in the body. It's a way of cheating death. It can be given away sometimes, But Donna, became part of me. I had to take it all away, it was the only way to save her...”  
“But Doctor. My baby sister, she’s got vortex energy in her mind. That’s something not meant for humans.”  
“Yes, I know.” The Doctor said shyly.  
“She could be dying even slower and more painfully. We don’t know this!”   
“You’re right, but Mycroft. She’s alive.”   
“Doctor, I’d rather her be dead than suffering.”  
“If you want, for reassurance, I could do a couple of Time Lord tests.”   
“What do you mean? What do they test for?   
“Well, they aren’t exactly tests. They mentally search the patient, and if they are feeling anything. We will catch it.” The Doctor looked into Mycroft’s brown eyes. “I can mentally search her, Mycroft. I am really sorry for not thinking of this sooner, but this is really the best way to see what she has seen, unlock the memories hiding away.”  
“So, like her emotions?”   
“Well, yes, but at a higher level. Any pain, any loss. Infact, we can find out what it is she is looking at. What frightens her.” The Doctor began to think up a plan, or was he just going to wing it? No, he couldn’t do that. Not on his love’s sister…  
“And no tampering with anything, unless you are POSITIVE it's what will make her better?” This shocked the Doctor back into reality.   
“Yes, I promise.”  
“And I expect to be checked in with to consent whenever there is a plan change.”  
The Doctor gave a sad smile. “You can be there the whole time.” He put a hand on Mycroft’s shoulder. “But Mycroft,” Mycroft flinched, but eased up quickly at the touch he had not felt in so many years.  
“What is it?”  
“This process…” The Doctor paused, rethinking his words. “It’s going to cause pain.” Mycroft began to slowly shake his head back and forth, not quite being able to cope. “But she won't remember any of it, I swear.” He quickly added, trying to ease Mycroft.   
“What pain?”  
“We will be opening long lost memories, there is no stopping it. There is no way to predict what will happen.”  
“The worst memory she may have, that I am aware of, is mother and father walking out on us, she was three. Is there any way to avoid that specific one?” Mycroft looked worried. “It was just around the time you came.”  
“There may be a way, but if you love her, Mycroft, let me help Alissa.”  
“Of course. Anything. We shall begin the process tomorrow at three in the afternoon precisely. At my Manor, I trust you know where that is?” The Doctor just smiled.   
“I shall prepare a room, is there special equipment you need provided?  
“No, except make sure there is somewhere she can lay down, incase there is need. It may be best to not let her know what it is we shall be doing...... But I will let you decide that.”  
“Okay.” Mycroft kissed the Doctor cautiously on the cheek. “I trust you, can you take me to Sherlock's flat? To pick her up, so she can get some sleep.”   
The Doctor got up and flipped a few switches on the console. “We’re here. Mind if I come in?”  
“Do, follow me. My sister will probably listen more attentively to your instructions after the previous epidemic. And I will tell Sherlock about our plan later on.” The Doctor nods then opens the doors, the two exit the T.A.R.D.I.S and walk into and up the stairs of 221B, opening the door cautiously to see John sitting in the living room with a tear-stained Alissa. Sherlock was in the kitchen making Alissa some tea. John gives a disapproving look to Mycroft, then turns to Alissa. “It’s okay Liss.” John turned back to the two standing in the doorway, “Please, come in.” The Doctor kneels next to Alissa, she wipes away a tear. “I’m sorry. You were right. We weren’t listening to eachother.”  
“Obviously, Myc could always be so ignorant and self centered. And you, Doctor-” She stood up to go into the kitchen with Sherlock. The Doctor looked over to Mycroft, still standing in the door.  
“If you want, there's a room at the Manor waiting for you, and if not there's plenty of rooms on the T.A.R.D.I.S.,” he said gently.  
The Doctor looked back to Alissa, “Yeah. You’re always welcome.” Sherlock is catching on to what the two were going to be doing, he opened his mouth, about to give away everything. Mycroft and the Doctor simultaneously gave Sherlock a serious glare, mouthing the words “No.” Sherlock closed his mouth and went back to making tea. Alissa replies, “I shall stay at the manor tonight. It's been months since I've been.” The Doctor scratched his head, “Yeah, yeah. Good. Would you two like a lift?” Mycroft agree’s. The Doctor escorts the two Holmes’ to the Police Box. Mycroft helps run the T.A.R.D.I.S, dusting off the file about such in his mind palace.” The Doctor smiles, “Thank you Mycroft.”   
“My pleasure.”   
“We are here, I’ll come see you two tomorrow.” He gives a concerning look to Mycroft. Mycroft follows his sister out of the T.A.R.D.I.S, but not before giving the Doctor a quick peck on the lips. The Doctor tries to dismiss the urge to smile, but failed badly in the end.


	3. Chapter 3

Mycroft is sitting on the sofa, drinking tea, the T.A.R.D.I.S materializes in front of him. The doors open and the Doctor steps forward. “Hello Doctor.” said Mycroft, standing up.   
“Hello Mycroft.” The Doctor rocked on his heels. “Where is Alissa?”   
“She's gone to bed, said she wanted to lay down. It is 9:30 after all.” The Doctor looked to his police box and rolled his eyes. “True.” He spun back around.  
“So I believe we have some business regarding our, relationship to discuss.” Said Mycroft sitting back down.   
“Right. Yes.” The Doctor stood in place, making a mental map of the room.  
“So what are we, exactly? Last time I saw you we were raising my siblings together, falling in love, and now we've had one of the biggest fights I've ever been in…”  
“We’ll figure this whole mess out, I promise.”  
“I know it will take a while for things to go back to what they were before, but I'd like to start over. If that's alright with you.”   
“I’d like that.” He smiled. “Have you-umm. Have you found anyone?”  
“Not since you left. No, like I said, I waited for you.” Mycroft is talking in the nicest possible  tone.  
“I thought about you the whole time I was away.” The Doctor said trying to ease Mycroft.  
“Me too. I mean- about you. Not myself.” The Doctor grinned very happily at this remark.  
“I have missed your sense of humor. Would bring me out of the darkest of days.”  
           “Doctor?”  
“Yes?”   
“I'd like to travel with you more.You know, next time you leave. Just you and me, travelling the stars together.”  
“Just the two of us.” The Doctor is sitting next to Mycroft now. Alissa walks through the arched doors yawning. Mycroft looked to his sleepy sister, “I thought you were going to bed Lissy.”  
“Couldn't sleep.” She turns to the Doctor. “What are you doing here Doctor? I thought you were coming around later.” Mycroft answered for him.

“I needed to talk to him about some things.”   
“What things? Are you back together or something?”

“Uhh.” The Doctor looks from Alissa to Mycroft. Mycroft looks at the Doctor with a look that says 'just say yes'  
“Yeah, yeah...Umm...We are trying to at least.” Alissa smiles.  
“Cool! Myc was always happier when he talked about you. Sherlock says he was happier when he was around you, too.”  
“Yeah, well I always enjoyed your company.”   
“Me too. Oh, I almost forgot what I came in here for, I'm going to order a pizza, would either of you like some?”   
“No thanks.” Mycroft shook his head.   
“Alright, well, see you two tomorrow.” She walks out the door again and into the kitchen.   
The Doctor looks to Mycroft. “What? What is it?”  
“Did you see how she looked at us?  
“What do you mean?”  
“Mm, probably nothing. Not everything is something.” Mycroft nods and looks down at his watch. “Oh, my. It's getting quite late. Would you like to stay here? You don't have to, but if you wanted to take a break from living in the T.A.R.D.I.S…”  
“Thank you, that would be nice.”  
“Excellent! If you want you can sleep in my room, but if you'd rather we have plenty of space.”   
“Oh, anywhere will do. I can even go sleep on top of the fridge if it is wanted.” The Doctor replies jokingly.  
“So, is that a yes you'd like to stay in my room?”

“What about you? Don't you usually sleep in your room?”

**“Well, yeah,” Mycroft fiddles with his watch. “But my bed is plenty big.” The Doctor smiles at Mycroft. He smiles back “Well, come on then.” Mycroft takes the Doctor’s hand and leads him to his room. The Doctor kisses Mycroft on the cheek. Mycroft is obviously blushing, but he turns his head so the Doctor’s and his lips meet. The Doctor is surprised and a little bit startled. Mycroft pulls away and opens the door to his bedroom. Mycroft drops the Doctor’s hand and rummages through a drawer, then shoves a pair of pajamas to him. “here, you can wear these.” The Doctor looks confused, as he normally just wears his suit to bed and changes in the morning. “It’ll be more comfortable, I promise.”  
            “Thank you, Mycroft.”   
“Of course.” Mycroft get’s into bed, as he is already wearing pajamas. He folds back the duvet on the other side for the Doctor.   
The Doctor is standing in place, looking around the room for a place to change. Mycroft looks up because of the silence coming from his friend. Realizing what was happening, Mycroft suggested he go into the closet, It’s a walk in. The Doctor makes an embarrassed little laugh, and walks over to the closet. Moments later, he returns out from the closet. “Right.” The Doctor climbs into bed. “Goodnight Mycroft.”  
“Good night, Doctor.” **


End file.
